Open source software and web services for designing therapeutic molecules G. P. S. Raghava, Head Bioinformatics Centre, Institute of Microbial Technology, Chandigarh Important Web Sites Open Source Drug Discovery(OSDD) CRDD Site: Raghava’s Group:

Software Development for Drug Discovery Discovery of Drug by Public for Public Drugs for Disease Specific to Developing Countries (like India) Development of Drugs for diseases of poor persons Process of Discovery will be fast (few to many contributors) Academic institutes/universities and small industry may afford

Examples of open source software Operating Systems –Linux –FreeBSD, OpenBSD, and NetBSD Internet –Apache (> 50% of the world's web servers) –BIND: DNS for the entire Internet. –Sendmail (Most servers) –OpenSSL (standard for secure communication) Programming Tools – Languages (Perl, Python, PHP) –GNU compilers and tools (GCC, Make)

The amount of fund required depends on the success rate at the clinical trial stage

An overview of the workflow of in silico drug designing process

Important Points 1.Source of Molecules (databases or repositories) 2.Molecular Editors (editing & viewing existing molecules) 3.Analog Generators (software used to generate analogs) 4.Structure Optimization (Energy/geometry of molecules) 5.Calculation of Molecular Descriptors 6.Chemical Similarity Search 7.Development of QSAR/QSPR Models 8.Classification and Clustering of Small Molecules 9.Docking Small Molecules in Macromolecules 10.Pharmacophore Tools/Search 11.Software for ADMET Techniques 12. Designing of Inhibitors 13.Major Initiatives towards affordable drugs

Databases and resources managing and hosting chemical compounds

List of major molecular editors, frequently used for drawing and editing molecules

Analogs generation softwares

List of software and web servers used for structure optimization of molecules

Important software and webserver for computing molecular descriptors

Similarity search algorithms and their web links

Machine learning and feature selection techniques in cheminformatics

List of chemical clustering tools and their web addresses

Different types of pharmocophore searching softwares

Some open source initiatives for drug discovery with their research area

Platform for Discovering and Designing of Drug Molecules Load Data Calculate descriptors CDK Padel ADMET Properties MetaPred ToxiPred DrugMint Screening Databases FDA molecules PUBChem Zinc datbase Format coversion SMILE MOL SDF Babel Pharmacophore